A novel superfamily containing the β-grasp fold involved in binding diverse soluble ligands

BACKGROUND: Domains containing the β-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS: Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the β-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins transcobalamin and intrinsic factor, the bacterial polysaccharide export proteins, the competence DNA receptor ComEA, the cob(I)alamin generating enzyme PduS and the Nqo1 subunit of the respiratory electron transport chain. We present evidence that members of this superfamily are likely to bind a range of soluble ligands, including B12. There are two major clades within this superfamily, namely the transcobalamin-like clade and the Nqo1-like clade. The former clade is typified by an insert of a β-hairpin after the helix of the β-grasp fold, whereas the latter clade is characterized by an insert between strands 4 and 5 of the core fold. CONCLUSION: Members of both clades within this superfamily are predicted to interact with ligands in a similar spatial location, with their specific inserts playing a role in the process. Both clades are widely represented in bacteria suggesting that this superfamily was derived early in bacterial evolution. The animal lineage appears to have acquired the transcobalamin-like proteins from low GC Gram-positive bacteria, and this might be correlated with the emergence of the ability to utilize B12 produced by gut bacteria. REVIEWERS: This article was reviewed by Andrei Osterman, Igor Zhulin, and Arcady Mushegian

Does the Box-Cox transformation help in forecasting macroeconomic time series?

The paper investigates whether transforming a time series leads to an improvement in forecasting accuracy. The class of transformations that is considered is the Box-Cox power transformation, which applies to series measured on a ratio scale. We propose a nonparametric approach for estimating the optimal transformation parameter based on the frequency domain estimation of the prediction error variance, and also conduct an extensive recursive forecast experiment on a large set of seasonal monthly macroeconomic time series related to industrial production and retail turnover. In about one fifth of the series considered the Box-Cox transformation produces forecasts significantly better than the untransformed data at one-step-ahead horizon; in most of the cases the logarithmic transformation is the relevant one. As the forecast horizon increases, the evidence in favour of a transformation becomes less strong. Typically, the naïve predictor that just reverses the transformation leads to a lower mean square error than the optimal predictor at short forecast leads. We also discuss whether the preliminary in-sample frequency domain assessment conducted provides a reliable guidance which series should be transformed for improving significantly the predictive performance

A Nonparametric Method for the Derivation of α/β Ratios from the Effect of Fractionated Irradiations

Multifractionation isoeffect data are commonly analysed under the assumption that cell survival determines the observed tissue or tumour response, and that it follows a linear-quadratic dose dependence. The analysis is employed to derive the α/β ratios of the linear-quadratic dose dependence, and different methods have been developed for this purpose. A common method uses the so-called Fe plot. A more complex but also more rigorous method has been introduced by Lam et al. (1979). Their method, which is based on numerical optimization procedures, is generalized and somewhat simplified in the present study. Tumour-regrowth data are used to explain the nonparametric procedure which provides α/β ratios without the need to postulate analytical expressions for the relationship between cell survival and regrowth delay

Dual-time-point FDG PET/CT imaging in prosthetic heart valve endocarditis

Purpose: FDG PET/CT has been of increasing interest in the diagnostic workup of prosthetic heart valve endocarditis (PVE). Some reports advocate later imaging time points to improve the diagnostic accuracy for PVE. In this study, we compared standard and late FDG PET/CT images in patients with a clinical suspicion of PVE. Materials and Methods: Fourteen scans in 13 patients referred for FDG PET/CT for suspicion of PVE performed at standard (60 min post injection) and late (150 min post injection) time points were scored based on visual interpretation and semi-quantitatively with SUVmax and target-to-background ratio (TBR, defined as [SUVmax valve/SUVmean blood pool]). Final diagnosis was based on surgical findings in all cases of infection (n = 6) and unremarkable follow-up in all others (n = 8). Results: Late images were more prone to false positive interpretation for both visual and semi-quantitative analyses. Visual analysis of the standard images yielded 1 false negative and 1 false positive result. On the late images, no scans were false negative but 5 scans were false positive. Conclusion: Late FDG PET/CT imaging for PVE seem

Glucose-induced fibronectin and collagen type III expression in renal fibroblasts can occur independent of TGF-β1

Glucose-induced fibronectin and collagen type III expression in renal fibroblasts can occur independent of TGF-β1.BackgroundVarious renal cell types have been shown to contribute to the excessive matrix deposition observed in diabetic nephropathy. The present study examined the effect of high ambient glucose and transforming growth factor-β1 (TGF-β1) on matrix production by human renal fibroblasts.MethodsHuman renal fibroblasts (TK173) were used to examine the effects of high glucose and TGF-β1 on fibronectin and collagen type III expression. Stable transfectants were generated of TK173 cells expressing a dominant negative TGF-β type II receptor. Matrix components were measured in enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR).ResultsFibronectin secretion by renal fibroblasts was increased upon exposure to high glucose, but with delayed kinetics compared to TGF-β1-induced fibronectin. Exposure to high glucose resulted in an increased secretion of latent TGF-β1. However, treatment with neutralizing pan-specific anti-TGF-β antibodies could not attenuate the effects of glucose. Furthermore, collagen type III was up-regulated by high glucose, but not by TGF-β1. Importantly, fibroblasts expressing a dominant negative TGF-β type II receptor were defective in TGF-β1-induced fibronectin production, whereas glucose-induced fibronectin and collagen type III were unaffected.ConclusionsThese data show that in renal fibroblasts exposure to high glucose can increase matrix production independent of endogenous TGF-β1. Although glucose activation is accompanied by an increased production of latent TGF-β1, which can have an important role in vivo, the data suggest involvement of alternative growth factors in the mechanism by which hyperglycemic conditions can modulate matrix accumulation in diabetic nephropathy

The Prognostic Value of Eight Immunohistochemical Markers Expressed in the Tumor Microenvironment and on Hodgkin Reed-Sternberg Cells in Pediatric Patients With Classical Hodgkin Lymphoma

Immunohistochemical markers are associated with treatment outcome in adults with classical Hodgkin Lymphoma (cHL). Studies in children are scarce and inconsistent. We investigated in 67 children with cHL, whether the expression of CD15, CD30, PAX5, PD-1, PD-L1, CD68, CD163 and TARC at diagnosis is associated with disease free survival (DFS) and with interim remission status. Low CD15 and low TARC expression were associated with relapsed disease. Low expression of PD-L1 was associated with complete remission at interim PET-scan. Our data suggest a difference between pediatric and adult cHL. This underlines the importance of future research into specific prognostic factors in pediatric cHL, indispensable for improvement of treatment in this population

Ex Vivo Expanded Multi-Specific Cytotoxic T Lymphocytes Derived from HIV+ Patients and HIV Negative Donors Using GMP Compliant Methodologies Recognize Multiple HIV Antigens and Suppress HIV Replication

Coderch de Sentmenat, José Antoni

Estimating the proportion of clinical mastitis attributable to subclinical mastitis in dairy cattle using two multivariable statistical approaches

The aim of this study was to quantify the proportion of first bovine CM cases attributable to high composite somatic cell counts (CSCC). Cows were followed from the first CSCC measurement postpartum until CM or censoring, using survival analysis. A conditional logistic regression model was also fitted to the data with CM cows being matched to cows without CM. Both models identified high CSCC cows to have a higher risk for subsequent CM cases than low CSCC cows. The population attributable fraction was 0.22 for primiparae and 0.17 for multiparae according to the logistic regression model, while it was 0.25 in the survival analysis. The latter approach also identified that the proportion of cows without CM would increase from 89% to 93%. Both multivariable statistical approaches showed that a substantial reduction in CM can be achieved by decreasing the prevalence of high CSCC in the dairy population

Schwinger-Keldysh Approach to Disordered and Interacting Electron Systems: Derivation of Finkelstein's Renormalization Group Equations

We develop a dynamical approach based on the Schwinger-Keldysh formalism to derive a field-theoretic description of disordered and interacting electron systems. We calculate within this formalism the perturbative RG equations for interacting electrons expanded around a diffusive Fermi liquid fixed point, as obtained originally by Finkelstein using replicas. The major simplifying feature of this approach, as compared to Finkelstein's is that instead of $N \to 0$ replicas, we only need to consider N=2 species. We compare the dynamical Schwinger-Keldysh approach and the replica methods, and we present a simple and pedagogical RG procedure to obtain Finkelstein's RG equations.Comment: 22 pages, 14 figure

Normal imaging findings after aortic valve implantation on 18F-Fluorodeoxyglucose positron emission tomography with computed tomography

Background: To determine the normal perivalvular 18F-Fluorodeoxyglucose (18F-FDG) uptake on positron emission tomography (PET) with computed tomography (CT) within one year after aortic prosthetic heart valve (PHV) implantation. Methods: Patients with uncomplicated aortic PHV implantation were prospectively included and underwent 18F-FDG PET/CT at either 5 (± 1) weeks (group 1), 12 (± 2) weeks (group 2) or 52 (± 8) weeks (group 3) after implantation. 18F-FDG uptake around the PHV was scored qualitatively (none/low/intermediate/high) and quantitatively by measuring the maximum Standardized Uptake Value (SUVmax) and target to background ratio (SUVratio). Results: In total, 37 patients (group 1: n = 12, group 2: n = 12, group 3: n = 13) (mean age 66 ± 8 years) were prospectively included. Perivalvular 18F-FDG uptake was low (8/12 (67%)) and intermediate (4/12 (33%)) in group 1, low (7/12 (58%)) and intermediate (5/12 (42%)) in group 2, and low (8/13 (62%)) and intermediate (5/13 (38%)) in group 3 (P = 0.91). SUVmax was 4.1 ± 0.7, 4.6 ± 0.9 and 3.8 ± 0.7 (mean ± SD, P = 0.08), and SUVratio was 2.0 [1.9 to 2.2], 2.0 [1.8 to 2.6], and 1.9 [1.7 to 2.0] (median [IQR], P = 0.81) for groups 1, 2, and 3, respectively. Conclusion: Non-infected aortic PHV have similar low to intermediate perivalvular 18F-FDG uptake with similar SUVmax and SUVratio at 5, 12, and 52 weeks after implantation